I also have a 2011 Limited with a 3rd row. Used to put everything in a big plastic bin, but it slid around too much, took up too much space, and I couldn't use one of the 3rd row seats. I've since switched to a duffel bag and it's so much better.
Fits everything that was in the bin previously and doesn't slide around at all. It takes up less space and is much easier to take out. For what it's worth, I keep jumper cables, breaker bar, ratchet straps, full 3/8" and 1/2" socket set, screwdrivers, duct tape, hatchet, MV50 compressor, fire extinguisher, and a ton of other miscellaneous stuff.
When I need both 3rd row seats, I just take everything out of the bag and place them through the rear window between the rear of the seats and the tailgate. Just gotta remember they're back there before opening the rear.
I use the contents of the duffel as often as I use the 3rd row. So it's no big inconvenience when I need to utilize either.